So what happens? Well, I head into "Main CSS" and edit a single table CSS setting. I save this single table CSS, and sometimes this causes my header-template to revert back to the first / original template file. This is causing me headaches because I often change the header template for different reasons.
Yet stranger is that it don't seem to always do this. Just sometimes... like every 10 times.
It is only the header-template that is affected by this.
//EDIT: for some reason it happened when editing another template (old phpinclude_start) in version 3.5 after the update. it reverted it back to the very first one after the upgrade.